[2024-01-24 10:57:38,855] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:38,857] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:38,857] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f68166c-31a9-40b9-96f4-423d6eecd4a3/dqc_reference
[2024-01-24 10:57:40,245] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:40,246] [INFO] Task started: Prodigal
[2024-01-24 10:57:40,247] [INFO] Running command: gunzip -c /var/lib/cwl/stge09d7ed5-1e03-4cc1-9533-46007f4c2788/GCF_018531375.1_ASM1853137v1_genomic.fna.gz | prodigal -d GCF_018531375.1_ASM1853137v1_genomic.fna/cds.fna -a GCF_018531375.1_ASM1853137v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:50,376] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:50,377] [INFO] Task started: HMMsearch
[2024-01-24 10:57:50,377] [INFO] Running command: hmmsearch --tblout GCF_018531375.1_ASM1853137v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f68166c-31a9-40b9-96f4-423d6eecd4a3/dqc_reference/reference_markers.hmm GCF_018531375.1_ASM1853137v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:50,664] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:50,666] [INFO] Found 6/6 markers.
[2024-01-24 10:57:50,700] [INFO] Query marker FASTA was written to GCF_018531375.1_ASM1853137v1_genomic.fna/markers.fasta
[2024-01-24 10:57:50,700] [INFO] Task started: Blastn
[2024-01-24 10:57:50,700] [INFO] Running command: blastn -query GCF_018531375.1_ASM1853137v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f68166c-31a9-40b9-96f4-423d6eecd4a3/dqc_reference/reference_markers.fasta -out GCF_018531375.1_ASM1853137v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:52,116] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:52,120] [INFO] Selected 14 target genomes.
[2024-01-24 10:57:52,121] [INFO] Target genome list was writen to GCF_018531375.1_ASM1853137v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:52,126] [INFO] Task started: fastANI
[2024-01-24 10:57:52,127] [INFO] Running command: fastANI --query /var/lib/cwl/stge09d7ed5-1e03-4cc1-9533-46007f4c2788/GCF_018531375.1_ASM1853137v1_genomic.fna.gz --refList GCF_018531375.1_ASM1853137v1_genomic.fna/target_genomes.txt --output GCF_018531375.1_ASM1853137v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:06,298] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:06,299] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f68166c-31a9-40b9-96f4-423d6eecd4a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:06,299] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f68166c-31a9-40b9-96f4-423d6eecd4a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:06,311] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:06,311] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:06,312] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	100.0	1247	1247	95	conclusive
Cellulomonas gilvus	strain=ATCC 13127	GCA_000218545.1	11	11	type	True	84.2384	892	1247	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	83.9709	873	1247	95	below_threshold
Cellulomonas gelida	strain=NBRC 3748	GCA_006538725.1	1712	1712	type	True	83.9063	873	1247	95	below_threshold
Cellulomonas gelida	strain=JCM 1490	GCA_014647015.1	1712	1712	type	True	83.7905	909	1247	95	below_threshold
Cellulomonas persica	strain=NBRC 101101	GCA_007989825.1	76861	76861	type	True	83.7891	871	1247	95	below_threshold
Cellulomonas uda	strain=NBRC 3747	GCA_006538705.1	1714	1714	type	True	83.7451	799	1247	95	below_threshold
Cellulomonas fimi	strain=ATCC 484	GCA_000212695.1	1708	1708	type	True	81.6082	803	1247	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	81.5754	794	1247	95	below_threshold
Cellulomonas terrae	strain=NBRC 100819	GCA_007990265.1	311234	311234	type	True	80.9873	738	1247	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	80.6964	682	1247	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	80.6335	746	1247	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	79.516	646	1247	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	79.3312	556	1247	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:06,313] [INFO] DFAST Taxonomy check result was written to GCF_018531375.1_ASM1853137v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:06,314] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:06,314] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:06,314] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f68166c-31a9-40b9-96f4-423d6eecd4a3/dqc_reference/checkm_data
[2024-01-24 10:58:06,315] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:06,352] [INFO] Task started: CheckM
[2024-01-24 10:58:06,352] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018531375.1_ASM1853137v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018531375.1_ASM1853137v1_genomic.fna/checkm_input GCF_018531375.1_ASM1853137v1_genomic.fna/checkm_result
[2024-01-24 10:59:05,002] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:05,004] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:05,025] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:05,025] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:05,025] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018531375.1_ASM1853137v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:05,026] [INFO] Task started: Blastn
[2024-01-24 10:59:05,026] [INFO] Running command: blastn -query GCF_018531375.1_ASM1853137v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f68166c-31a9-40b9-96f4-423d6eecd4a3/dqc_reference/reference_markers_gtdb.fasta -out GCF_018531375.1_ASM1853137v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:07,519] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:07,522] [INFO] Selected 13 target genomes.
[2024-01-24 10:59:07,522] [INFO] Target genome list was writen to GCF_018531375.1_ASM1853137v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:07,531] [INFO] Task started: fastANI
[2024-01-24 10:59:07,531] [INFO] Running command: fastANI --query /var/lib/cwl/stge09d7ed5-1e03-4cc1-9533-46007f4c2788/GCF_018531375.1_ASM1853137v1_genomic.fna.gz --refList GCF_018531375.1_ASM1853137v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018531375.1_ASM1853137v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:20,556] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:20,572] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:20,573] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_018531375.1	s__Cellulomonas sp018531375	100.0	1247	1247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000218545.1	s__Cellulomonas gilvus	84.241	892	1247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538725.1	s__Cellulomonas gelida	83.9229	871	1247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.61	99.23	0.96	0.91	3	-
GCF_007989825.1	s__Cellulomonas persica	83.8307	867	1247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538705.1	s__Cellulomonas uda	83.7657	798	1247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	98.69	98.01	0.94	0.90	4	-
GCF_007990245.1	s__Cellulomonas composti	82.8128	788	1247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004306155.1	s__Cellulomonas biazotea	81.7503	707	1247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000212695.1	s__Cellulomonas fimi	81.5258	812	1247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	99.99	1.00	1.00	3	-
GCF_001462455.1	s__Cellulomonas sp001462455	81.2682	684	1247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007990265.1	s__Cellulomonas terrae	81.0839	727	1247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018623035.1	s__Cellulomonas sp018623035	80.6568	678	1247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.51	99.03	0.98	0.95	3	-
GCF_013409305.1	s__Cellulomonas soli	80.617	698	1247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004886325.1	s__Cellulomonas telluris	80.5878	752	1247	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:20,574] [INFO] GTDB search result was written to GCF_018531375.1_ASM1853137v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:20,575] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:20,578] [INFO] DFAST_QC result json was written to GCF_018531375.1_ASM1853137v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:20,578] [INFO] DFAST_QC completed!
[2024-01-24 10:59:20,579] [INFO] Total running time: 0h1m42s